Okay National Review answered my question for me and even tested their answer:
“UPDATE: Ive confirmed that scanning an image, converting it to a PDF, optimizing that PDF, and then opening it up in Illustrator, does in fact create layers similar to what is seen in the birth certificate PDF. You can try it yourself at home.”
http://www.nationalreview.com/corner/265767/pdf-layers-obamas-birth-certificate-nathan-goulding
Im glad they followed up on this and tested it as well. Thank you NRO!
...I tried the same thing with a doc I scanned and...
...I didn't get "Deleted or cropped content (1 item)"...
...but then again I only play an expert on TV... ;^)